1
|
Rauf A, Sher MA, Farooq U, Rasheed A, Sajjad M, Jing R, Khan Z, Attia KA, Mohammed AA, Fiaz S, Chen J, Rehman SU. An SNP based genotyping assay for genes associated with drought tolerance in bread wheat. Mol Biol Rep 2024; 51:527. [PMID: 38637351 DOI: 10.1007/s11033-024-09481-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND SnRK2 plays vital role in responding to adverse abiotic stimuli. The applicability of TaSnRK2.4 and TaSnRK2.9 was investigated to leverage the potential of these genes in indigenous wheat breeding programs. METHODS Genetic diversity was assessed using pre-existing markers for TaSnRK2.4 and TaSnRK2.9. Furthermore, new markers were also developed to enhance their broader applicability. KASP markers were designed for TaSnRK2.4, while CAPS-based markers were tailored for TaSnRK2.9. RESULTS Analysis revealed lack of polymorphism in TaSnRK2.4 among Pakistani wheat germplasm under study. To validate this finding, available gel-based markers for TaSnRK2.4 were employed, producing consistent results and offering limited potential for application in marker-assisted wheat breeding with Pakistani wheat material. For TaSnRK2.9-5A, CAPS2.9-5A-1 and CAPS2.9-5A-2 markers were designed to target SNP positions at 308 nt and 1700 nt revealing four distinct haplotypes. Association analysis highlighted the significance of Hap-5A-1 of TaSnRK2.9-5A, which exhibited association with an increased number of productive tillers (NPT), grains per spike (GPS), and reduced plant height (PH) under well-watered (WW) conditions. Moreover, it showed positive influence on NPT under WW conditions, GPS under water-limited (WL) conditions, and PH under both WW and WL conditions. High selection intensity observed for Hap-5A-1 underscores the valuable role it has played in Pakistani wheat breeding programs. Gene expression studies of TaSnRK2.9-5A revealed the involvement of this gene in response to PEG, NaCl, low temperature and ABA treatments. CONCLUSION These findings propose that TaSnRK2.9 can be effectively employed for improving wheat through marker-assisted selection in wheat breeding efforts.
Collapse
Affiliation(s)
- Abdul Rauf
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
- SINO-PAK Joint Research Laboratory, MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Ali Sher
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Umar Farooq
- Department of Food Science and Technology, MNS University of Agriculture, Multan, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Riyadh, 11451, Saudi Arabia
| | - Arif Ahmed Mohammed
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Riyadh, 11451, Saudi Arabia
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, the University of Haripur, Haripur, 22620, Pakistan
| | - Jing Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan.
- SINO-PAK Joint Research Laboratory, MNS University of Agriculture, Multan, Pakistan.
| |
Collapse
|
2
|
Qin R, Cao M, Dong J, Chen L, Guo H, Guo Q, Cai Y, Han L, Huang Z, Xu N, Yang A, Xu H, Wu Y, Sun H, Liu X, Ling H, Zhao C, Li J, Cui F. Fine mapping of a major QTL, qKl-1BL controlling kernel length in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:67. [PMID: 38441674 DOI: 10.1007/s00122-024-04574-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/03/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE A major stable QTL, qKl-1BL, for kernel length of wheat was narrowed down to a 2.04-Mb interval on chromosome 1BL; the candidate genes were predicated and the genetic effects on yield-related traits were characterized. As a key factor influencing kernel weight, wheat kernel shape is closely related to yield formation, and in turn affects both wheat processing quality and market value. Fine mapping of the major quantitative trait loci (QTL) for kernel shape could provide genetic resources and a theoretical basis for the genetic improvement of wheat yield-related traits. In this study, a major QTL for kernel length (KL) on 1BL, named qKl-1BL, was identified from the recombinant inbred lines (RIL) in multiple environments based on the genetic map and physical map, with 4.76-21.15% of the phenotypic variation explained. To fine map qKl-1BL, the map-based cloning strategy was used. By using developed InDel markers, the near-isogenic line (NIL) pairs and eight key recombinants were identified from a segregating population containing 3621 individuals derived from residual heterozygous lines (RHLs) self-crossing. In combination with phenotype identification, qKl-1BL was finely positioned into a 2.04-Mb interval, KN1B:698.15-700.19 Mb, with eight differentially expressed genes enriched at the key period of kernel elongation. Based on transcriptome analysis and functional annotation information, two candidate genes for qKl-1BL controlling kernel elongation were identified. Additionally, genetic effect analysis showed that the superior allele of qKl-1BL from Jing411 could increase KL, thousand kernel weight (TKW), and yield per plant (YPP) significantly, as well as kernel bulk density and stability time. Taken together, this study identified a QTL interval for controlling kernel length with two possible candidate genes, which provides an important basis for qKl-1BL cloning, functional analysis, and application in molecular breeding programs.
Collapse
Affiliation(s)
- Ran Qin
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Mingsu Cao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jizi Dong
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Linqu Chen
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Haoru Guo
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Qingjie Guo
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yibiao Cai
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Lei Han
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Zhenjie Huang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Ninghao Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Aoyu Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Huiyuan Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yongzhen Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Han Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050000, China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunhua Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050000, China.
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
| |
Collapse
|
3
|
López-Fernández M, García-Abadillo J, Uauy C, Ruiz M, Giraldo P, Pascual L. Genome wide association in Spanish bread wheat landraces identifies six key genomic regions that constitute potential targets for improving grain yield related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:244. [PMID: 37957405 PMCID: PMC10643358 DOI: 10.1007/s00122-023-04492-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
KEY MESSAGE Association mapping conducted in 189 Spanish bread wheat landraces revealed six key genomic regions that constitute stable QTLs for yield and include 15 candidate genes. Genetically diverse landraces provide an ideal population to conduct association analysis. In this study, association mapping was conducted in a collection of 189 Spanish bread wheat landraces whose genomic diversity had been previously assessed. These genomic data were combined with characterization for yield-related traits, including grain size and shape, and phenological traits screened across five seasons. The association analysis revealed a total of 881 significant marker trait associations, involving 434 markers across the genome, that could be grouped in 366 QTLs based on linkage disequilibrium. After accounting for days to heading, we defined 33 high density QTL genomic regions associated to at least four traits. Considering the importance of detecting stable QTLs, 6 regions associated to several grain traits and thousand kernel weight in at least three environments were selected as the most promising ones to harbour targets for breeding. To dissect the genetic cause of the observed associations, we studied the function and in silico expression of the 413 genes located inside these six regions. This identified 15 candidate genes that provide a starting point for future analysis aimed at the identification and validation of wheat yield related genes.
Collapse
Affiliation(s)
- Matilde López-Fernández
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering (ETSIAAB), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Julián García-Abadillo
- Department of Biotechnology and Plant Biology, Centre for Biotechnology and Plant Genomics (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Magdalena Ruiz
- Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), CSIC, Autovía A2, Km. 36.2. Finca La Canaleja, 28805, Alcalá de Henares, Madrid, Spain
| | - Patricia Giraldo
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering (ETSIAAB), Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering (ETSIAAB), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| |
Collapse
|
4
|
Ali I, Anwar S, Ali A, Ullah Z, Binjawhar DN, Sher H, Abdel-Hameed UK, Khan MA, Majeed K, Jaremko M. Biochemical and phenological characterization of diverse wheats and their association with drought tolerance genes. BMC PLANT BIOLOGY 2023; 23:326. [PMID: 37331960 DOI: 10.1186/s12870-023-04278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/11/2023] [Indexed: 06/20/2023]
Abstract
Drought is one of the most important wheat production limiting factor, and can lead to severe yield losses. This study was designed to examine the effect of drought stress on wheat physiology and morphology under three different field capacities (FC) viz. 80% (control), 50% (moderate) and 30% (severe drought stress) in a diverse collection of wheat germplasm including cultivars, landraces, synthetic hexaploid and their derivatives. Traits like grain weight, thousand grain weight and biomass were reduced by 38.23%, 18.91% and 26.47% respectively at 30% FC, whereas the reduction rate for these traits at 50% FC were 19.57%, 8.88% and 18.68%. In principal component analysis (PCA), the first two components PC1 and PC2 accounted for 58.63% of the total variation and separated the cultivars and landraces from synthetic-based germplasm. Landraces showed wide range of phenotypic variations at 30% FC compared to synthetic-based germplasm and improved cultivars. However, least reduction in grain weight was observed in improved cultivars which indicated the progress in developing drought resilient cultivars. Allelic variations of the drought-related genes including TaSnRK2.9-5A, TaLTPs-11, TaLTPs-12, TaSAP-7B-, TaPPH-13, Dreb-B1 and 1fehw3 were significantly associated with the phenological traits under drought stress in all 91 wheats including 40 landraces, 9 varieties, 34 synthetic hexaploids and 8 synthetic derivatives. The favorable haplotypes of 1fehw3, Dreb-B1, TaLTPs-11 and TaLTPs-12 increased grain weight, and biomass. Our results iterated the fact that landraces could be promising source to deploy drought adaptability in wheat breeding. The study further identified drought tolerant wheat genetic resources across various backgrounds and identified favourable haplotypes of water-saving genes which should be considered to develop drought tolerant varieties.
Collapse
Affiliation(s)
- Iftikhar Ali
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, 999077, Hong Kong.
| | - Saeed Anwar
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan
| | - Ahmad Ali
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan.
| | - Zahid Ullah
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan
| | - Dalal Nasser Binjawhar
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11671, Saudi Arabia.
| | - Hassan Sher
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan
| | - Usama K Abdel-Hameed
- Biology Department, College of Science, Taibah University, Al-Madinah Al-Munawarah, 42353, Saudi Arabia
- Botany Department, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | | | - Khawar Majeed
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 329555-6900, Saudi Arabia
| |
Collapse
|
5
|
Reddy SS, Saini DK, Singh GM, Sharma S, Mishra VK, Joshi AK. Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1166439. [PMID: 37251775 PMCID: PMC10213333 DOI: 10.3389/fpls.2023.1166439] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/14/2023] [Indexed: 05/31/2023]
Abstract
Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.
Collapse
Affiliation(s)
- S Srinatha Reddy
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - G Mahendra Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Joshi
- Borlaug Institute of South Asia (BISA), NASC Complex, DPS Marg, New Delhi, India
- CIMMYT, NASC Complex, DPS Marg, New Delhi, India
| |
Collapse
|
6
|
Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
Collapse
Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
| |
Collapse
|
7
|
Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.). Genes (Basel) 2023; 14:genes14030637. [PMID: 36980909 PMCID: PMC10048783 DOI: 10.3390/genes14030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three environments. A total of 26 marker-trait associations (MTAs) were detected on 18 chromosomes covering the A, B, and D subgenomes of bread wheat. The GPC showed the maximum MTAs (16), followed by NDVI (6), and TKW (4). A maximum of 10 MTAs was located on the B subgenome, whereas, 8 MTAs each were mapped on the A and D subgenomes. In silico analysis suggest that the SNPs were located on important putative candidate genes such as NAC domain superfamily, zinc finger RING-H2-type, aspartic peptidase domain, folylpolyglutamate synthase, serine/threonine-protein kinase LRK10, pentatricopeptide repeat, protein kinase-like domain superfamily, cytochrome P450, and expansin. These candidate genes were found to have different roles including regulation of stress tolerance, nutrient remobilization, protein accumulation, nitrogen utilization, photosynthesis, grain filling, mitochondrial function, and kernel development. The effects of newly identified MTAs will be validated in different genetic backgrounds for further utilization in marker-aided breeding.
Collapse
|
8
|
Flavell RB. A framework for improving wheat spike development and yield based on the master regulatory TOR and SnRK gene systems. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:755-768. [PMID: 36477879 PMCID: PMC9899413 DOI: 10.1093/jxb/erac469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The low rates of yield gain in wheat breeding programs create an ominous situation for the world. Amongst the reasons for this low rate are issues manifested in spike development that result in too few spikelets, fertile florets, and therefore grains being produced. Phases in spike development are particularly sensitive to stresses of various kinds and origins, and these are partly responsible for the deficiencies in grain production and slow rates of gain in yield. The diversity of developmental processes, stresses, and the large numbers of genes involved make it particularly difficult to prioritize approaches in breeding programs without an overarching, mechanistic framework. Such a framework, introduced here, is provided around the master regulator target of rapamycin and sucrose non-fermenting-1 (SNF1)-related protein kinase complexes and their control by trehalose-6-phosphate and other molecules. Being master regulators of the balance between growth and growth inhibition under stress, these provide genetic targets for creating breakthroughs in yield enhancement. Examples of potential targets and experimental approaches are described.
Collapse
|
9
|
Khan N, Zhang Y, Wang J, Li Y, Chen X, Yang L, Zhang J, Li C, Li L, Ur Rehman S, Reynolds MP, Zhang L, Zhang X, Mao X, Jing R. TaGSNE, a WRKY transcription factor, overcomes the trade-off between grain size and grain number in common wheat and is associated with root development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6678-6696. [PMID: 35906966 DOI: 10.1093/jxb/erac327] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/26/2022] [Indexed: 05/28/2023]
Abstract
Wheat is one of the world's major staple food crops, and breeding for improvement of grain yield is a priority under the scenarios of climate change and population growth. WRKY transcription factors are multifaceted regulators in plant growth, development, and responses to environmental stimuli. In this study, we identify the WRKY gene TaGSNE (Grain Size and Number Enhancer) in common wheat, and find that it has relatively high expression in leaves and roots, and is induced by multiple abiotic stresses. Eleven single-nucleotide polymorphisms were identified in TaGSNE, forming two haplotypes in multiple germplasm collections, named as TaGSNE-Hap-1 and TaGSNE-Hap-2. In a range of different environments, TaGSNE-Hap-2 was significantly associated with increases in thousand-grain weight (TGW; 3.0%) and spikelet number per spike (4.1%), as well as with deeper roots (10.1%) and increased root dry weight (8.3%) at the mid-grain-filling stage, and these were confirmed in backcross introgression populations. Furthermore, transgenic rice lines overexpressing TaGSNE had larger panicles, more grains, increased grain size, and increased grain yield relative to the wild-type control. Analysis of geographic and temporal distributions revealed that TaGSNE-Hap-2 is positively selected in China and Pakistan, and TaGSNE-Hap-1 in Europe. Our findings demonstrate that TaGSNE overcomes the trade-off between TGW/grain size and grain number, leading us to conclude that these elite haplotypes and their functional markers could be utilized in marker-assisted selection for breeding high-yielding varieties.
Collapse
Affiliation(s)
- Nadia Khan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Genetics, University of Karachi, Pakistan
| | - Yanfei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuying Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lili Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shoaib Ur Rehman
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan 60000, Pakistan
| | | | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
10
|
Nisar T, Tahir MHN, Iqbal S, Sajjad M, Nadeem MA, Qanmber G, Baig A, Khan Z, Zhao Z, Geng Z, Ur Rehman S. Genome-wide characterization and sequence polymorphism analyses of cysteine-rich poly comb-like protein in Glycine max. FRONTIERS IN PLANT SCIENCE 2022; 13:996265. [PMID: 36204049 PMCID: PMC9531024 DOI: 10.3389/fpls.2022.996265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Cysteine-rich poly comb-like protein (CPP) is a member of cysteine-rich transcription factors that regulates plant growth and development. In the present work, we characterized twelve CPP transcription factors encoding genes in soybean (Glycine max). Phylogenetic analyses classified CPP genes into six clades. Sequence logos analyses between G. max and G. soja amino acid residues exhibited high conservation. The presence of growth and stress-related cis-acting elements in the upstream regions of GmCPPs highlight their role in plant development and tolerance against abiotic stress. Ka/Ks levels showed that GmCPPs experienced limited selection pressure with limited functional divergence arising from segmental or whole genome duplication events. By using the PAN-genome of soybean, a single nucleotide polymorphism was identified in GmCPP-6. To perform high throughput genotyping, a kompetitive allele-specific PCR (KASP) marker was developed. Association analyses indicated that GmCPP-6-T allele of GmCPP-6 (in exon region) was associated with higher thousand seed weight under both water regimes (well-water and water-limited). Taken together, these results provide vital information to further decipher the biological functions of CPP genes in soybean molecular breeding.
Collapse
Affiliation(s)
- Tayyaba Nisar
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan, Pakistan
| | - Muhammad Hammad Nadeem Tahir
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan, Pakistan
| | - Shahid Iqbal
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad, Islamabad, Pakistan
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ayesha Baig
- Department of Biotechnology, Commission on Science and Technology for Sustainable Development in the South (COMSATS), University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan, Pakistan
| | - Zhengyun Zhao
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Zhide Geng
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan, Pakistan
| |
Collapse
|
11
|
Khan H, Krishnappa G, Kumar S, Mishra CN, Krishna H, Devate NB, Rathan ND, Parkash O, Yadav SS, Srivastava P, Biradar S, Kumar M, Singh GP. Genome-wide association study for grain yield and component traits in bread wheat ( Triticum aestivum L.). Front Genet 2022; 13:982589. [PMID: 36092913 PMCID: PMC9458894 DOI: 10.3389/fgene.2022.982589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
Collapse
Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonu Singh Yadav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Suma Biradar
- University of Agricultural Sciences, Dharwad, India
| | - Monu Kumar
- ICAR-Indian Agricultural Research Institute, Jharkhand, India
| | | |
Collapse
|
12
|
Majeed U, Hou J, Hao C, Zhang X. TaNAC020 homoeologous genes are associated with higher thousand kernel weight and kernel length in Chinese wheat. Front Genet 2022; 13:956921. [PMID: 36092915 PMCID: PMC9458977 DOI: 10.3389/fgene.2022.956921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
NAC proteins constitute one of the largest plant-specific transcription factor (TF) families and play significant roles in plant growth and development. In the present study, three TaNAC020 homoeologous genes located on chromosomes 7A, 7B, and 7D were isolated from wheat (Triticum aestivum L.). TaNAC020s were predominantly expressed in developing grains. The developed transgenic rice lines for TaNAC020-B showed higher starch density and lower amylose contents than those of the wild type (WT). Sequence polymorphism studies showed seven and eight SNPs in TaNAC020-A/B, making three and two haplotypes, respectively. No sequence polymorphism was identified in TaNAC020-D. Association analysis revealed that HAP-2 of TaNAC020-A and TaNAC020-B was the favored haplotype for higher thousand kernel weight and length. Geographic distribution and allelic frequency showed that our favored haplotype experienced strong selection in China, and likewise, diversity increased in TaNAC020s during wheat polyploidization. The results obtained in this study demonstrate that TaNAC020s positively influence starch synthesis and accumulation and are one of the key regulators of the kernel (seed) size and kernel number and have the potential for utilization in wheat breeding to improve grain yield. Molecular markers developed in this study stand instrumental in marker-assisted selection for genetic improvement and germplasm enhancement in wheat.
Collapse
|
13
|
Fatima C, Tahir MHN, Ikram RM, Khan Z, Sajjad M, Qanmber G, Darwish E, Geng Z, Xiangkuo G, Ur Rehman S. Characterization of Histone H3 Gene Family Reveals That GmHH3-3 is Associated With Higher Seed Weight in Glycine max. Front Genet 2022; 13:949027. [PMID: 35937992 PMCID: PMC9353304 DOI: 10.3389/fgene.2022.949027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 11/23/2022] Open
Abstract
The main function of histone protein is to provide support to the structure of chromosomes. It helps in binding a long thread of DNA into a more condensed shape to fit into the nucleus. From histone variants, histone H3 (HH3) plays a crucial role in plant growth and development. Characterization of histones has not been reported in Glycine max till now. The objective of this study was to characterize the HH3 gene family for molecular breeding of G. max. In this study, 17 HH3 members in G. max were identified by performing local BLASTp using HH3 members from Arabidopsis as a query. Phylogenetic analysis classified HH3 genes in seven clades. Sequence logo analysis among Arabidopsis thaliana, Oryza sativa, and Glycine max showed a higher level of similarity in amino acids. Furthermore, conserveness of G. max HH3 genes was also confirmed by Gene Structure Display. Ten paralogous gene pairs were identified in GmHH3 genes in the Glycine max genome by conducting collinearity analysis. G. max HH3 genes have experienced strong purifying selection pressure, with limited functional divergence originating from the segmental and whole-genome duplication, as evidenced by the Ka/Ks ratio. The KASP marker was developed for GmHH3-3 gene. Genotyping was performed on 46 G. max genotypes. This differentiation was based upon the presence of either GmHH3-3-C or GmHH3-3-T allele in the CDS region. The results showed that G. max accessions containing the GmHH3-3-T allele at respective locus showed higher thousand seed weight than that of those accessions that contain the GmHH3-3-C allele. This research provides the basic information to further decipher the function of HH3 in soybean.
Collapse
Affiliation(s)
- Chahat Fatima
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | | | | | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Essam Darwish
- Plant Physiology Section, Agricultural Botany Department, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhide Geng
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Gao Xiangkuo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
- *Correspondence: Gao Xiangkuo, ; Shoaib Ur Rehman,
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
- *Correspondence: Gao Xiangkuo, ; Shoaib Ur Rehman,
| |
Collapse
|
14
|
Wang C, Zhang L, Xie Y, Guo X, Zhang Y, Zhang Y, Irshad A, Li Y, Qian H, Jing D, Liu G, Wu K, Yang N, Yang G, Song Y, Guo H, Zhao H, Wang C, Liu L, Zhang G, Ma S. A superior allele of the wheat gene TaGL3.3-5B, selected in the breeding process, contributes to seed size and weight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1879-1891. [PMID: 35377004 DOI: 10.1007/s00122-022-04081-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
A superior allele of wheat gene TaGL3.3-5B was identified and could be used in marker-assisted breeding in wheat. Identifying the main genes which mainly regulate the yield-associated traits can significantly increase the wheat production. In this study, gene TaGL3.3 was cloned from common wheat according to the sequence of OsPPKL3. A SNP in the 8th exon of TaGL3.3-5B, T/C in coding sequence (CDS), which resulted in an amino acid change (Val/Ala), was identified between the low 1000-kernel weight (TKW) wheat Chinese Spring and the high TKW wheat Xinong 817 (817). Subsequently, association analysis in the mini-core collection (MCC) and the recombinant inbred lines (RIL) revealed that the allele TaGL3.3-5B-C (from 817) was significantly correlated with higher TKW. The high frequency of TaGL3.3-5B-C in the Chinese modern wheat cultivars indicated that it was selected positively in wheat breeding programs. The overexpression of TaGL3.3-5B-C in Arabidopsis resulted in shorter pods and longer grains than those of wild-type counterparts. Additionally, TaGL3.3 expressed a tissue-specific pattern in wheat as revealed by qRT-PCR. We also found that 817 showed higher expression of TaGL3.3 than that in Chinese Spring (CS) during the seed development. These results demonstrate that TaGL3.3 plays an important role in the formation of seed size and weight. Allele TaGL3.3-5B-C is associated with larger and heavier grains that are beneficial to wheat yield improvement.
Collapse
Affiliation(s)
- Chaojie Wang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Lili Zhang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, 712100, Shaanxi, People's Republic of China
- College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Xiaofeng Guo
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yanfang Zhang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yamin Zhang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ahsan Irshad
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Yuting Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Huihui Qian
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Doudou Jing
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Guangyao Liu
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Kaiming Wu
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Na Yang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Guoli Yang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yulong Song
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Huiyan Zhao
- College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chengshe Wang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China.
| | - Gaisheng Zhang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Shoucai Ma
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, 712100, Shaanxi, People's Republic of China.
| |
Collapse
|
15
|
Qiao L, Li H, Wang J, Zhao J, Zheng X, Wu B, Du W, Wang J, Zheng J. Analysis of Genetic Regions Related to Field Grain Number per Spike From Chinese Wheat Founder Parent Linfen 5064. FRONTIERS IN PLANT SCIENCE 2022; 12:808136. [PMID: 35069666 PMCID: PMC8769526 DOI: 10.3389/fpls.2021.808136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Wheat founder parents have been important in the development of new wheat cultivars. Understanding the effects of specific genome regions on yield-related traits in founder variety derivatives can enable more efficient use of these genetic resources through molecular breeding. In this study, the genetic regions related to field grain number per spike (GNS) from the founder parent Linfen 5064 were analyzed using a doubled haploid (DH) population developed from a cross between Linfen 5064 and Nongda 3338. Quantitative trait loci (QTL) for five spike-related traits over nine experimental locations/years were identified, namely, total spikelet number per spike (TSS), base sterile spikelet number per spike (BSSS), top sterile spikelet number per spike (TSSS), fertile spikelet number per spike (FSS), and GNS. A total of 13 stable QTL explaining 3.91-19.51% of the phenotypic variation were found. The effect of six of these QTL, Qtss.saw-2B.1, Qtss.saw-2B.2, Qtss.saw-3B, Qfss.saw-2B.2, Qbsss.saw-5A.1, and Qgns.saw-1A, were verified by another DH population (Linfen 5064/Jinmai 47), which showed extreme significance (P < 0.05) in more than three environments. No homologs of reported grain number-related from grass species were found in the physical regions of Qtss.saw-2B.1 and Qtss.saw-3B, that indicating both of them are novel QTL, or possess novel-related genes. The positive alleles of Qtss.saw-2B.2 from Linfen 5064 have the larger effect on TSS (3.30%, 0.62) and have 66.89% in Chinese cultivars under long-term artificial selection. This study revealed three key regions for GNS in Linfen 5064 and provides insights into molecular marker-assisted breeding.
Collapse
Affiliation(s)
- Ling Qiao
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Hanlin Li
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jie Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Weijun Du
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
| | - Juanling Wang
- College of Agronomy, State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Jinzhong, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| |
Collapse
|
16
|
Li Y, Tang J, Liu W, Yan W, Sun Y, Che J, Tian C, Zhang H, Yu L. The Genetic Architecture of Grain Yield in Spring Wheat Based on Genome-Wide Association Study. Front Genet 2021; 12:728472. [PMID: 34868206 PMCID: PMC8634730 DOI: 10.3389/fgene.2021.728472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/30/2021] [Indexed: 11/24/2022] Open
Abstract
Uncovering the genetic architecture for grain yield (GY)–related traits is important for wheat breeding. To detect stable loci for GY-related traits, a genome-wide association study (GWAS) was conducted in a diverse panel, which included 251 elite spring wheat accessions mainly from the Northeast of China. In total, 52,503 single nucleotide polymorphisms (SNPs) from the wheat 55 K SNP arrays were used. Thirty-eight loci for GY-related traits were detected and each explained 6.5–16.7% of the phenotypic variations among which 12 are at similar locations with the known genes or quantitative trait loci and 26 are likely to be new. Furthermore, six genes possibly involved in cell division, signal transduction, and plant development are candidate genes for GY-related traits. This study provides new insights into the genetic architecture of GY and the significantly associated SNPs and accessions with a larger number of favorable alleles could be used to further enhance GY in breeding.
Collapse
Affiliation(s)
- Yuyao Li
- Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingquan Tang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wenlin Liu
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wenyi Yan
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yan Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingyu Che
- Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Chao Tian
- Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Hongji Zhang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lihe Yu
- Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
17
|
Irshad A, Guo H, Ur Rehman S, Wang X, Gu J, Xiong H, Xie Y, Zhao L, Zhao S, Wang C, Liu L. Identification of Single Nucleotide Polymorphism in TaSBEIII and Development of KASP Marker Associated With Grain Weight in Wheat. Front Genet 2021; 12:697294. [PMID: 34306037 PMCID: PMC8299302 DOI: 10.3389/fgene.2021.697294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022] Open
Abstract
Manipulation of genes involved in starch synthesis could significantly affect wheat grain weight and yield. The starch-branching enzyme (SBE) catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via an α-1,6 linkage. Three types of SBE isoforms (SBEI, SBEII, and SBEIII) exist in higher plants, with the number of SBE isoforms being species-specific. In this study, the coding sequence of the wheat TaSBEIII gene was amplified. After the multiple sequence alignment of TaSBEIII genome from 20 accessions in a wheat diversity panel, one SNP was observed in TaSBEIII-A, which formed the allelic marker allele-T. Based on this SNP at 294 bp (C/T), a KASP molecular marker was developed to distinguish allelic variation among the wheat genotypes for thousand grain weight (TGW). The results were validated using 262 accessions of mini core collection (MCC) from China, 153 from Pakistan, 53 from CIMMYT, and 17 diploid and 18 tetraploid genotypes. Association analysis between TaSBEIII-A allelic variation and agronomic traits found that TaSBEIII-A was associated with TGW in mini core collection of China (MCC). The accessions possessing Allele-T had higher TGW than those possessing Allele-C; thus, Allele-T was a favorable allelic variation. By analyzing the frequency of the favorable allelic variation Allele-T in MCC, it increased from pre-1950 (25%) to the 1960s (45%) and increased continuously from 1960 to 1990 (80%). The results suggested that the KASP markers can be utilized in grain weight improvement, which ultimately improves wheat yield by marker-assisted selection in wheat breeding. The favorable allelic variation allele-T should be valuable in enhancing grain yield by improving the source and sink simultaneously. Furthermore, the newly developed KASP marker validated in different genetic backgrounds could be integrated into a breeding kit for screening high TGW wheat.
Collapse
Affiliation(s)
- Ahsan Irshad
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan, Pakistan
| | - Xueqing Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Chaojie Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| |
Collapse
|
18
|
Association between the Polymorphisms of fads2a and fads2b and Poly-Unsaturated Fatty Acids in Common Carp ( Cyprinus carpio). Animals (Basel) 2021; 11:ani11061780. [PMID: 34203588 PMCID: PMC8232129 DOI: 10.3390/ani11061780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary Fishes are the major dietary source of polyunsaturated fatty acids (PUFAs) for humans. The limited availability of PUFAs derived from fish represents a critical bottleneck in food production systems, one that numerous research institutions and aqua-feed companies in this field are trying to overcome. This problem could be minimized by select-bred fish to be capable of more effectively producing endogenous PUFAs. Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in the synthesis of PUFAs. The common carp, one of the most important food and ornamental allo-tetraploid fish, encodes two fads2 genes (fads2a and fads2b). The PUFA contents among common carp individuals were numerous, suggesting that there might exist polymorphisms in fads2a and fads2b. However, selective breeding of common carp with high PUFA contents was hindered due to a lack of effective molecular markers. This study investigated the contents of PUFAs in common carp and identified polymorphisms in the CDS regions of fads2a and fads2b. The association study identified three cSNPs associated with the PUFA contents and suggested that fads2b might be the major gene responding for common carp PUFA contents. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp. Abstract Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one fads2, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (fads2a and fads2b). The associations between the contents of different PUFAs and the polymorphisms of fads2a and fads2b have not been studied. The contents of 12 PUFAs in common carp individuals were measured, and the polymorphisms in the coding sequences of fads2a and fads2b were screened. We identified five coding single nucleotide polymorphisms (cSNPs) in fads2a and eleven cSNPs in fads2b. Using the mixed linear model and analysis of variance, a synonymous fads2a cSNP was significantly associated with the content of C20:3n-6. One non-synonymous fads2b cSNP (fads2b.751) and one synonymous fads2b cSNP (fads2b.1197) were associated with the contents of seven PUFAs and the contents of six PUFAs, respectively. The heterozygous genotypes in both loci were associated with higher contents than the homozygous genotypes. The fads2b.751 genotype explained more phenotype variation than the fads2b.1197 genotype. These two SNPs were distributed in one haplotype block and associated with the contents of five common PUFAs. These results suggested that fads2b might be the major gene responding to common carp PUFA contents and that fads.751 might be the main effect SNP. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp.
Collapse
|
19
|
Ur Rehman S, Ali Sher M, Saddique MAB, Ali Z, Khan MA, Mao X, Irshad A, Sajjad M, Ikram RM, Naeem M, Jing R. Development and Exploitation of KASP Assays for Genes Underpinning Drought Tolerance Among Wheat Cultivars From Pakistan. Front Genet 2021; 12:684702. [PMID: 34178041 PMCID: PMC8220157 DOI: 10.3389/fgene.2021.684702] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
High-throughput genotyping for functional markers offers an excellent opportunity to effectively practice marker-assisted selection (MAS) while breeding cultivars. We developed kompetitive allele-specific PCR (KASP) assays for genes conferring drought tolerance in common wheat (Triticum aestivum L.). In total, 11 KASP assays developed in this study and five already reported assays were used for their application in wheat breeding. We investigated alleles at 16 loci associated with drought tolerance among 153 Pakistani hexaploid wheat cultivars released during 1953-2016; 28 diploid wheat accessions (16 for AA and 12 for BB) and 19 tetraploid wheat (AABB) were used to study the evolutionary history of the studied genes. Superior allelic variations of the studied genes were significantly associated with higher grain yield. Favored haplotypes of TaSnRK2.3-1A, TaSnRK2.3-1B, TaSnRK2.9-5A, TaSAP-7B, and TaLTPs-1A predominated in Pakistani wheat germplasm indicating unconscious pyramiding and selection pressure on favorable haplotypes during selection breeding. TaSnRK2.8-5A, TaDreb-B1, 1-feh w3, TaPPH-7A, TaMOC-7A, and TaPARG-2A had moderate to low frequencies of favorable haplotype among Pakistani wheat germplasm pointing toward introgression of favorable haplotypes by deploying functional markers in marker-assisted breeding. The KASP assays were compared with gel-based markers for reliability and phenotypically validated among 62 Pakistani wheat cultivars. Association analyses showed that the favorable allelic variations were significantly associated with grain yield-contributing traits. The developed molecular marker toolkit of the genes can be instrumental for the wheat breeding in Pakistan.
Collapse
Affiliation(s)
- Shoaib Ur Rehman
- Institiute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Muhammad Ali Sher
- Institiute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Muhammad Abu Bakar Saddique
- Institiute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Zulfiqar Ali
- Institiute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Mahmood Alam Khan
- Institiute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahsan Irshad
- National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Rao Muhammad Ikram
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Mahnoor Naeem
- Institiute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
20
|
Genome-Wide Identification and Expression Analyses of AnSnRK2 Gene Family under Osmotic Stress in Ammopiptanthus nanus. PLANTS 2021; 10:plants10050882. [PMID: 33925572 PMCID: PMC8145913 DOI: 10.3390/plants10050882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 11/29/2022]
Abstract
Sucrose non-fermenting-1 (SNF1)-related protein kinase 2’s (SnRK2s) are plant-specific serine/threonine protein kinases and play crucial roles in the abscisic acid signaling pathway and abiotic stress response. Ammopiptanthus nanus is a relict xerophyte shrub and extremely tolerant of abiotic stresses. Therefore, we performed genome-wide identification of the AnSnRK2 genes and analyzed their expression profiles under osmotic stresses including drought and salinity. A total of 11 AnSnRK2 genes (AnSnRK2.1-AnSnRK2.11) were identified in the A. nanus genome and were divided into three groups according to the phylogenetic tree. The AnSnRK2.6 has seven introns and others have eight introns. All of the AnSnRK2 proteins are highly conserved at the N-terminus and contain similar motif composition. The result of cis-acting element analysis showed that there were abundant hormone- and stress-related cis-elements in the promoter regions of AnSnRK2s. Moreover, the results of quantitative real-time PCR exhibited that the expression of most AnSnRK2s was induced by NaCl and PEG-6000 treatments, but the expression of AnSnRK2.3 and AnSnRK2.6 was inhibited, suggesting that the AnSnRK2s might play key roles in stress tolerance. The study provides insights into understanding the function of AnSnRK2s.
Collapse
|
21
|
Mo Z, Zhu J, Wei J, Zhou J, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Li W, Wei Y, Zheng Y, Lan X, Ma J. The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat ( Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:732837. [PMID: 34531890 PMCID: PMC8439258 DOI: 10.3389/fpls.2021.732837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace "Ailanmai" × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.
Collapse
Affiliation(s)
- Ziqiang Mo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xiujin Lan
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jian Ma
| |
Collapse
|
22
|
Cao J, Shang Y, Xu D, Xu K, Cheng X, Pan X, Liu X, Liu M, Gao C, Yan S, Yao H, Gao W, Lu J, Zhang H, Chang C, Xia X, Xiao S, Ma C. Identification and Validation of New Stable QTLs for Grain Weight and Size by Multiple Mapping Models in Common Wheat. Front Genet 2020; 11:584859. [PMID: 33262789 PMCID: PMC7686802 DOI: 10.3389/fgene.2020.584859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Improvement of grain weight and size is an important objective for high-yield wheat breeding. In this study, 174 recombinant inbred lines (RILs) derived from the cross between Jing 411 and Hongmangchun 21 were used to construct a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq). Three mapping methods, including inclusive composite interval mapping (ICIM), genome-wide composite interval mapping (GCIM), and a mixed linear model performed with forward-backward stepwise (NWIM), were used to identify QTLs for thousand grain weight (TGW), grain width (GW), and grain length (GL). In total, we identified 30, 15, and 18 putative QTLs for TGW, GW, and GL that explain 1.1-33.9%, 3.1%-34.2%, and 1.7%-22.8% of the phenotypic variances, respectively. Among these, 19 (63.3%) QTLs for TGW, 10 (66.7%) for GW, and 7 (38.9%) for GL were consistent with those identified by genome-wide association analysis in 192 wheat varieties. Five new stable QTLs, including 3 for TGW (Qtgw.ahau-1B.1, Qtgw.ahau-4B.1, and Qtgw.ahau-4B.2) and 2 for GL (Qgl.ahau-2A.1 and Qgl.ahau-7A.2), were detected by the three aforementioned mapping methods across environments. Subsequently, five cleaved amplified polymorphic sequence (CAPS) markers corresponding to these QTLs were developed and validated in 180 Chinese mini-core wheat accessions. In addition, 19 potential candidate genes for Qtgw.ahau-4B.2 in a 0.31-Mb physical interval were further annotated, of which TraesCS4B02G376400 and TraesCS4B02G376800 encode a plasma membrane H+-ATPase and a serine/threonine-protein kinase, respectively. These new QTLs and CAPS markers will be useful for further marker-assisted selection and map-based cloning of target genes.
Collapse
Affiliation(s)
- Jiajia Cao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Yaoyao Shang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Dongmei Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Kangle Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xinran Cheng
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xu Pan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xue Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Mingli Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Chang Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shengnan Yan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Hui Yao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wei Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jie Lu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Haiping Zhang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Cheng Chang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shihe Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chuanxi Ma
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| |
Collapse
|
23
|
Shoaib M, Yang W, Shan Q, Sun L, Wang D, Sajjad M, Li X, Sun J, Liu D, Zhan K, Zhang A. TaCKX gene family, at large, is associated with thousand-grain weight and plant height in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3151-3163. [PMID: 32852585 DOI: 10.1007/s00122-020-03661-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
KEY MESSAGE We used SMRT sequencing and explored the haplotypes of TaCKX genes, linked with thousand-grain weight and plant height, and developed the functionally validated markers, which can be used in the marker-assisted breeding program. Cytokinin oxidase/dehydrogenase (CKX) enzymes catalyze the permanent degradation of cytokinins. Identification of the TaCKX alleles associated with yield traits and the development of functional markers is the first step in using these alleles in marker-assisted breeding program. To identify the alleles, we sequenced the genome fragments, containing TaCKX genes from 48 wheat genotypes, by PacBio® sequencing. Six out of 22 TaCKX genes were found polymorphic, forming 14 distinct haplotypes. Functional markers were developed and validated for all the polymorphic TaCKX genes. Four specific haplotypes, i.e., TaCKX2A_2, TaCKX4A_2, TaCKX5A_3, and TaCKX9A_2, were found significantly associated with high thousand-grain weight (TGW) and short plant height (PH) in Chinese wheat micro-core collection (MCC) and GWAS open population (GWAS-OP), whereas TaCKX1B_2 in GWAS-OP and TaCKX11A_3 in MCC were significantly associated with high TGW and short PH. The mean values of TGW and PH for cumulative favorable haplotypes from chromosome 3A, i.e., TaCKX2A_2, TaCKX4A_2, and TaCKX5A_3, were significantly higher as compared to the cumulative unfavored haplotypes, and the change was additive in manner. Frequency distribution analysis revealed that since the 1960s, the frequency of the favorable haplotypes and TGW has gradually increased in Chinese wheat cultivars. Expression profiling in the seed tissue excised at 2, 4, 6, and 8 days after anthesis depicted that the favorable haplotypes are significantly less expressive as compared to the unfavored haplotypes. We conclude that the functional markers developed in this study can be used to select the favorable haplotypes of TaCKX genes in wheat marker-assisted breeding programs.
Collapse
Affiliation(s)
- Muhammad Shoaib
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Qiangqiang Shan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- The Collaborative Innovation Center for Grain Crops in Henan, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Linhe Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Sajjad
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlaikalan, Islamabad, 45550, Pakistan
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kehui Zhan
- The Collaborative Innovation Center for Grain Crops in Henan, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
24
|
Liu N, Cheng F. Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. BMC PLANT BIOLOGY 2020; 20:245. [PMID: 32487017 PMCID: PMC7265254 DOI: 10.1186/s12870-020-02449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS). RESULTS The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%). CONCLUSIONS Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
Collapse
Affiliation(s)
- Na Liu
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fangyun Cheng
- Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
25
|
Cao S, Xu D, Hanif M, Xia X, He Z. Genetic architecture underpinning yield component traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1811-1823. [PMID: 32062676 DOI: 10.1007/s00122-020-03562-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.
Collapse
Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mamoona Hanif
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|
26
|
Rasheed A, Takumi S, Hassan MA, Imtiaz M, Ali M, Morgunov AI, Mahmood T, He Z. Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1503-1520. [PMID: 31897516 DOI: 10.1007/s00122-019-03523-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.
Collapse
Affiliation(s)
- Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Muhammad Adeel Hassan
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Mohsin Ali
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Alex I Morgunov
- International Maize and Wheat Improvement Center (CIMMYT), Yenimahalle, Ankara, 06170, Turkey
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| |
Collapse
|
27
|
Mao X, Li Y, Rehman SU, Miao L, Zhang Y, Chen X, Yu C, Wang J, Li C, Jing R. The Sucrose Non-Fermenting 1-Related Protein Kinase 2 (SnRK2) Genes Are Multifaceted Players in Plant Growth, Development and Response to Environmental Stimuli. PLANT & CELL PHYSIOLOGY 2020; 61:225-242. [PMID: 31834400 DOI: 10.1093/pcp/pcz230] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/20/2019] [Indexed: 05/28/2023]
Abstract
Reversible protein phosphorylation orchestrated by protein kinases and phosphatases is a major regulatory event in plants and animals. The SnRK2 subfamily consists of plant-specific protein kinases in the Ser/Thr protein kinase superfamily. Early observations indicated that SnRK2s are mainly involved in response to abiotic stress. Recent evidence shows that SnRK2s are multifarious players in a variety of biological processes. Here, we summarize the considerable knowledge of SnRK2s, including evolution, classification, biological functions and regulatory mechanisms at the epigenetic, post-transcriptional and post-translation levels.
Collapse
Affiliation(s)
- Xinguo Mao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, P. R. China
| | - Yuying Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
- College of Agronomy, Henan Agricultural University, Zhengzhou 450016, P. R. China
| | - Shoaib Ur Rehman
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan, Pakistan
| | - Lili Miao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Yanfei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
- College of Agronomy, Henan Agricultural University, Zhengzhou 450016, P. R. China
| | - Xin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Chunmei Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jingyi Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Chaonan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Ruilian Jing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| |
Collapse
|
28
|
Irshad A, Guo H, Zhang S, Gu J, Zhao L, Xie Y, Xiong H, Zhao S, Ding Y, Ma Y, Liu L. EcoTILLING Reveals Natural Allelic Variations in Starch Synthesis Key Gene TaSSIV and Its Haplotypes Associated with Higher Thousand Grain Weight. Genes (Basel) 2019; 10:genes10040307. [PMID: 31003564 PMCID: PMC6523294 DOI: 10.3390/genes10040307] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 01/18/2023] Open
Abstract
Wheat is a staple food commodity grown worldwide, and wheat starch is a valuable source of energy and carbon that constitutes 80% of the grain weight. Manipulation of genes involved in starch synthesis significantly affects wheat grain weight and yield. TaSSIV plays an important role in starch synthesis and its main function is granule formation. To mine and stack more favorable alleles, single nucleotide polymorphisms (SNPs) of TaSSIV-A, B, and D were investigated across 362 wheat accessions by Ecotype-Targeting Induced Local Lesions IN Genome (EcoTILLING). As a result, a total of 38 SNPs in the amplified regions of three TaSSIV genes were identified, of which 10, 15, and 13 were in TaSSIV-A, B, and D, respectively. These 38 SNPs were evaluated by using KASP and six SNPs showed an allele frequency >5% whereas the rest were <5%, i.e., considered to be minor alleles. In the Chinese mini core collection, three haplotypes were detected for TaSSIV–A and three for TaSSIV–B. The results of an association study in the Chinese mini core collection with thousand grain weight (TGW) and spike length (SPL) showed that Hap-2-1A was significantly associated with TGW and Hap-3-1B with SPL. Allelic frequency and geographic distribution indicated that the favored haplotype (Hap-2-1A) has been positively selected in Chinese wheat breeding. These results suggested that the Kompetitive Allele Specific PCR (KASP) markers can be applied in starch improvement to ultimately improve wheat yield by marker assisted selection in wheat breeding.
Collapse
Affiliation(s)
- Ahsan Irshad
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Shunlin Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Yuping Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
| |
Collapse
|